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Introduction to ATCC Microbiome Standards

Have you evaluated how the format (i.e., frozen versus lyophilized) of the ATCC® Microbiome Standards affects DNA extractability?

We compared the DNA extractability of freshly grown, frozen and lyophilized cultures that were prepared from the same starting number of cells and didn't see any significant differences in the quantity and quality of DNA recovered.

The ATCC website states that it is open to discussing collaborations. What type/level of collaboration are you looking for?

We are a private, nonprofit biological resource center and research organization and our mission focuses on the acquisition, authentication, production, preservation, development, and distribution of standard reference microorganisms, cell lines, and other materials for research in the life sciences. To fulfill our mission, we collaborate with scientists in academia and industry. We are interested in developing new standards for various novel applications. Please feel free to contact us to discuss specific collaboration opportunities.

If I include the whole cell ATCC® Microbiome Standard in my experimental procedure and discover that bias is introduced, how would I normalize that?

Using the whole cell standard could reveal several different types of bias or error:

The presence of false positives in the control library, which could potentially come from upstream contamination (e.g., "kit contaminants")

Drop out of one of the known control organisms

Bias in relative abundance/quantification; the whole cell standard is particularly useful for measuring this as it captures DNA extraction biases

The complementary analysis scorecard that is generated when using the One Codex data analysis platform is geared towards helping you understand which of the above biases you may have. By understanding which biases are present, you can make adjustments in either your wet lab or analytical protocols; this could range from computationally subtracting or masking identified "kit contaminant" organisms to modifying your DNA extraction with an eye towards your organisms of interest, etc.